Research workbench
De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
Analyse De novo design of protein homo-oligomers with modular hydrogen bond… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J0L
- Type
- protein
- Length
- 705 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Designed protein 3L6HC2_2
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 92% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Designed protein 3L6HC2_2 | protein | 130 | 91% helix, 0% strand | — |
| B | Designed protein 3L6HC2_2 | protein | 120 | 93% helix, 0% strand | — |
| C | Designed protein 3L6HC2_2 | protein | 118 | 95% helix, 0% strand | — |
| D | Designed protein 3L6HC2_2 | protein | 119 | 92% helix, 0% strand | — |
| E | Designed protein 3L6HC2_2 | protein | 111 | 91% helix, 0% strand | — |
| F | Designed protein 3L6HC2_2 | protein | 107 | 88% helix, 0% strand | — |
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.84 | 0.93 | 63 | empty |
| 2 | 307 | 0.83 | 0.93 | 63 | empty |
| 3 | 678 | 0.82 | 0.86 | 92 | empty |
| 4 | 870 | 0.76 | 0.80 | 73 | empty |
| 5 | 353 | 0.73 | 0.84 | 32 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1838 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1787 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1618 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 746 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 557 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5J0L · De novo design of protein homo-oligomers with modular hydrogen bond network-mediated… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5J0L · PDBe 5J0L
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